Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

[Oksana Korol]

Thanks for the detailed breakdown of the places to check, Carl! I was able
to fix the issue following the steps you've outlined. For the benefit of
other readers, here is what I did to fix it:

On Tue, Jan 26, 2016 at 10:09 AM, Carl Eberhard 
wrote:

> Hi, Oksana
>
> There are a few places to look and things to check in this situation.
>
> *First*, are other visualizations working on your production instance? Do
> you see the visualization icon/button and does the dropdown there have the
> 'charts' visualization on tabular files (like bed)?
>

Yes, I am able to see other visualizations.


>
> On the admin side for this, when your instance starts up you should see a
> section of logging data for visualizations that are loaded or error in the
> paster log. They're shown after the converter tools output logging info and
> before the job runners output theirs. They look something like:
>
> galaxy.web.base.pluginframework INFO 2016-01-26 09:57:37,989
> VisualizationsRegistry, loaded plugin: phyloviz
>
> You should see the standard visualizations load there including
> 'phyloviz'. If there's a problem, then you'll see a stack trace and a
> message saying that it was skipped.
>
Logs where showing no problems.


> *Second*, if visualizations are working well for other types, can you try
> uploading a phyloxml file and seeing if phyloviz will launch from that
> data? There's an example in this history:
>
> https://test.galaxyproject.org/u/carleberhard/h/phyloviz
>
Uploaded phyloxml sample and it was showing visualization icon.


> *Third*, it may be an issue with how the datatype is being referenced in
> the phyloviz config file (when compared with your datatypes_conf.xml file).
>
I've checked datatypes_conf.xml file and the lines that describe newick and
nexus datatypes where commented out. A bit silly, but that was what was
breaking it. Uncommenting them fixed the issue.

Thanks for all your help, guys!

Cheers,
Oksana
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Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

[Björn Grüning]

Hi,

can you please check this setting?

https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L270

Thanks,
Bjoern

Am 25.01.2016 um 15:46 schrieb Oksana Korol:
> Thanks, Bjoern!
> 
> For my local install of Galaxy, logging in as a user worked and the icon
> is showing up (although I still had to manually go and change
> permissions on all the mako templates in ./database/compiled_templates
> directory). But our production instance of Galaxy (also v15.07 on CentOS
> 6.7) does not show the chart-symbol for Phyloviz, even when I'm logged
> in as a user. In production, it is not a clean install, but an upgrade
> from previous versions, so it is harder to figure out what's going on.
> There are no errors in the logs, so I'm still looking for any kind of
> clues of what could have gone wrong with the visualization.
> 
> Cheers,
> Oksana
> 
> Message: 1
> Date: Sat, 23 Jan 2016 19:55:47 +0100
> From: Björn Grüning <bjoern.gruen...@gmail.com
> <mailto:bjoern.gruen...@gmail.com>>
> To: Oksana Korol <oko...@gmail.com <mailto:oko...@gmail.com>>,
> galaxy-dev@lists.galaxyproject.org
>     <mailto:galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS
> Message-ID: <56a3ccb3.9020...@gmail.com
> <mailto:56a3ccb3.9020...@gmail.com>>
> Content-Type: text/plain; charset=utf-8
> 
> Hi Oksana,
> 
> this work for me in 16.01 (upcoming). Please make sure you are logged
> into your Galaxy as some user, not anonymous and than the Phyloviz
> Visualisation will be available from the small chart-symbol next to the
> (i) symbol.
> 
> Hope this helps,
> Bjoern
> 
> Am 22.01.2016 um 23:53 schrieb Oksana Korol:
> > Hi,
> >
> > I'm having trouble getting visualization icons, like Phyloviz, to show
> > up on my Galaxy instance running in CentOS 6.7. Here are the steps I
> > took, expecting it to work:
> >
> > 1. cloned Galaxy tag v15.07 (that's the version we need to run in
> > production)
> >
> >  2. Followed the steps in
> https://wiki.galaxyproject.org/VisualizationSetup
> >   - Renamed datatypes_conf.xml.sample to
> > datatypes_conf.xml
> >   - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit
> >   - Installed BED Tools
> >   - Added above tools to my user path (galaxy_utils dir is where
> > wigToBigWig and others are):
> >
> 
> /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/*home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin
> > *
> > 3. Started Galaxy.
> >
> > 4. Uploaded a newick tree file (nhx), which is known to be displayable
> > in phyloviz on a Ubuntu instance of Galaxy
> >
> > 5. Made sure the datatype is nhx
> >
> > 6. Expecting to see a Phyloviz "graph" icon on the left, when I expand
> > the file in history, but there is nothing there.
> >
> > At this point I don't know where to dig to find how I can fix it. Any
> > feedback, including your own stories for visualization setup or how I
> > can debug what's not being picked up where, would be greatly
> appreciated.
> >
> > Cheers,
> > Oksana
> > --
> > ::
> > Oksana Korol
> > dataquarry.blogspot.ca <http://dataquarry.blogspot.ca>
> <http://dataquarry.blogspot.ca>
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/
> >
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> >
> 
> 
> 
> 
> ___
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> 
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Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

[Björn Grüning]

This gets tricky, can you check if the visualisations are loacted under
this path and do double-check the filetypes? The icon is only displayed
with the correct datatype.

Am 25.01.2016 um 17:37 schrieb Oksana Korol:
> It's un-commented in both local and production. Still there is no icon
> in production.
> 
> Cheers,
> Oksana
> 
> On Mon, Jan 25, 2016 at 9:52 AM, Björn Grüning
> <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> wrote:
> 
> Hi,
> 
> can you please check this setting?
> 
> 
> https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L270
> 
> Thanks,
> Bjoern
> 
> Am 25.01.2016 um 15:46 schrieb Oksana Korol:
> > Thanks, Bjoern!
> >
> > For my local install of Galaxy, logging in as a user worked and the icon
> > is showing up (although I still had to manually go and change
> > permissions on all the mako templates in ./database/compiled_templates
> > directory). But our production instance of Galaxy (also v15.07 on CentOS
> > 6.7) does not show the chart-symbol for Phyloviz, even when I'm logged
> > in as a user. In production, it is not a clean install, but an upgrade
> > from previous versions, so it is harder to figure out what's going on.
> > There are no errors in the logs, so I'm still looking for any kind of
> > clues of what could have gone wrong with the visualization.
> >
> > Cheers,
> > Oksana
> >
> > Message: 1
> > Date: Sat, 23 Jan 2016 19:55:47 +0100
> > From: Björn Grüning <bjoern.gruen...@gmail.com 
> <mailto:bjoern.gruen...@gmail.com>
> > <mailto:bjoern.gruen...@gmail.com
> <mailto:bjoern.gruen...@gmail.com>>>
> > To: Oksana Korol <oko...@gmail.com <mailto:oko...@gmail.com>
> <mailto:oko...@gmail.com <mailto:oko...@gmail.com>>>,
>     >     galaxy-dev@lists.galaxyproject.org
> <mailto:galaxy-dev@lists.galaxyproject.org>
> > <mailto:galaxy-dev@lists.galaxyproject.org
> <mailto:galaxy-dev@lists.galaxyproject.org>>
> > Subject: Re: [galaxy-dev] Setting up visualization on Galaxy on 
> CentOS
> > Message-ID: <56a3ccb3.9020...@gmail.com 
> <mailto:56a3ccb3.9020...@gmail.com>
> > <mailto:56a3ccb3.9020...@gmail.com
> <mailto:56a3ccb3.9020...@gmail.com>>>
> > Content-Type: text/plain; charset=utf-8
> >
> > Hi Oksana,
> >
> > this work for me in 16.01 (upcoming). Please make sure you are
> logged
> > into your Galaxy as some user, not anonymous and than the Phyloviz
> > Visualisation will be available from the small chart-symbol
> next to the
> > (i) symbol.
> >
> > Hope this helps,
> > Bjoern
> >
> > Am 22.01.2016 um 23:53 schrieb Oksana Korol:
> > > Hi,
> > >
> > > I'm having trouble getting visualization icons, like
> Phyloviz, to show
> > > up on my Galaxy instance running in CentOS 6.7. Here are the
> steps I
> > > took, expecting it to work:
> > >
> > > 1. cloned Galaxy tag v15.07 (that's the version we need to
> run in
> > > production)
> > >
> > >  2. Followed the steps in
> > https://wiki.galaxyproject.org/VisualizationSetup
> > >   - Renamed datatypes_conf.xml.sample to
> > > datatypes_conf.xml
> > >   - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit
> > >   - Installed BED Tools
> > >   - Added above tools to my user path (galaxy_utils dir is where
> > > wigToBigWig and others are):
> > >
> >   
>  
> /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/*home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin
> > > *
> > > 3. Started Galaxy.
> > >
> > > 4. Uploaded a newick tree file (nhx), which is known to be
> displayable
> > > in phyloviz on a Ubuntu instance of Galaxy
> > >
> > > 5. Made sure the datatype is nhx
> > >
> > > 6. Expecting to see a Phyloviz "graph" icon on the le

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

[Oksana Korol]

It get even trickier... I just double-checked my local install, and I
didn't have visualization_plugins_directory uncommented, and yet, it works
on local install

>This gets tricky, can you check if the visualisations are loacted under
>this path

If you mean phyoviz and other plugin code from github, then yes, it's
there. I doulbe-checked the files and permissions as well, just to be sure.

> and do double-check the filetypes? The icon is only displayed
> with the correct datatype.

I did... I use exactly the same newick tree file for local and for
production test. Upload it, selecting nhx as a datatype. Double-check the
datatype by clicking on a pencil icon - it's nhx on both, but it works on
local and doesn't on production.

I'll keep digging and comparing the two installs. If you think of anything
else, let me know.

Thanks!

Oksana
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Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

[Björn Grüning]

Hi Oksana,

this work for me in 16.01 (upcoming). Please make sure you are logged
into your Galaxy as some user, not anonymous and than the Phyloviz
Visualisation will be available from the small chart-symbol next to the
(i) symbol.

Hope this helps,
Bjoern

Am 22.01.2016 um 23:53 schrieb Oksana Korol:
> Hi,
> 
> I'm having trouble getting visualization icons, like Phyloviz, to show
> up on my Galaxy instance running in CentOS 6.7. Here are the steps I
> took, expecting it to work:
> 
> 1. cloned Galaxy tag v15.07 (that's the version we need to run in
> production)
> 
>  2. Followed the steps in https://wiki.galaxyproject.org/VisualizationSetup
>   - Renamed datatypes_conf.xml.sample to
> datatypes_conf.xml
>   - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit
>   - Installed BED Tools
>   - Added above tools to my user path (galaxy_utils dir is where
> wigToBigWig and others are):
> /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/*home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin
> *
> 3. Started Galaxy.
> 
> 4. Uploaded a newick tree file (nhx), which is known to be displayable
> in phyloviz on a Ubuntu instance of Galaxy
> 
> 5. Made sure the datatype is nhx
> 
> 6. Expecting to see a Phyloviz "graph" icon on the left, when I expand
> the file in history, but there is nothing there.
> 
> At this point I don't know where to dig to find how I can fix it. Any
> feedback, including your own stories for visualization setup or how I
> can debug what's not being picked up where, would be greatly appreciated.
> 
> Cheers,
> Oksana
> -- 
> ::
> Oksana Korol
> dataquarry.blogspot.ca 
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> 
___
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